Re: [deal.II] Re: Announcing the deal.II Code Gallery
Hi Jean-Paul,
Yes, Thanks! I removed all the CG examples except for
goal_oriented_electroplasticity and my own and it worked I guess it is
one of the CG examples.. It takes an painfully long time to write the html
on my puny macbook air :)
- Mike
On Tuesday, March 7, 2017 at 11:54:42 AM UTC-5, Jean-Paul Pelteret wrote:
>
> Thanks Wolfgang, a slight permutation of that seemed to work! I'll submit
> a PR in a moment.
>
> Michael, can you tell me if you've built any of the code gallery examples?
> I think that this might be the issue. If you have, can you go into those
> examples' directories and run "make distclean", then try to build the
> documentation again? It looks like this has fixed the problem for me.
>
> FYI. Before cleaning the CG examples completely, this was the last line of
> doxygen.log:
>
>> input buffer overflow, can't enlarge buffer because scanner uses REJECT
>>
>
> On Tuesday, March 7, 2017 at 5:34:39 PM UTC+1, Wolfgang Bangerth wrote:
>>
>> On 03/07/2017 09:30 AM, Jean-Paul Pelteret wrote:
>> >
>> > Matthias, is there any way to disable the deletion of doxygen.log when
>> a
>> > build of the documentation fails?
>>
>> In doc/doxygen/CMakeLists.txt, line ~230, you have
>>
>> ADD_CUSTOM_COMMAND(
>>OUTPUT
>> ${CMAKE_BINARY_DIR}/doxygen.log
>>COMMAND ${DOXYGEN_EXECUTABLE}
>> ${CMAKE_CURRENT_BINARY_DIR}/options.dox
>> > ${CMAKE_BINARY_DIR}/doxygen.log 2>&1 # *pssst*
>>...
>>
>> Can you try to change that into something of the form
>>
>> ADD_CUSTOM_COMMAND(
>>OUTPUT
>> ${CMAKE_BINARY_DIR}/doxygen.log
>>COMMAND
>> (${DOXYGEN_EXECUTABLE}
>> ${CMAKE_CURRENT_BINARY_DIR}/options.dox
>> > ${CMAKE_BINARY_DIR}/doxygen.log 2>&1 # *pssst*
>> )
>> ||
>> mv ${CMAKE_BINARY_DIR}/doxygen.log ${CMAKE_BINARY_DIR}/doxygen.err
>>...
>>
>>
>> The second branch of || is only executed if the first one fails, and
>> moves the output file to an error file.
>>
>> If this happens to work, please submit this as a patch in general -- we
>> should try to preserve error messages.
>>
>> Best
>> W.
>>
>> --
>>
>> Wolfgang Bangerth email: bang...@colostate.edu
>>
>> www: http://www.math.colostate.edu/~bangerth/
>>
>
--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
https://groups.google.com/d/forum/dealii?hl=en
---
You received this message because you are subscribed to the Google Groups
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Announcing the deal.II Code Gallery
Thanks! I am glad it wasn't just me!! Mike On Tuesday, March 7, 2017 at 10:26:43 AM UTC-5, Jean-Paul Pelteret wrote: > > Hi Michael, > > I've just tried to build the documentation with the code gallery and have > run into similar problems. I'm going to fiddle around to see if I can work > out what the issue might be. I'll post an update if I get anywhere with > this. > > Best, > Jean-Paul > > On Tuesday, March 7, 2017 at 3:50:46 PM UTC+1, Michael Harmon wrote: >> >> I ran "make" again and attached the outputs fm the terminal into make.log >> >> I also ran "make install" and attached the outputs from the into >> make_install.log >> >> It seems they are failing at different points... but I'm not sure whats >> going wrong.. >> >> Thanks, >> >> Mike >> >> On Monday, March 6, 2017 at 10:58:28 PM UTC-5, Wolfgang Bangerth wrote: >>> >>> On 03/06/2017 08:14 PM, Michael Harmon wrote: >>> > The doxygen.log file seems to get deleted... but here's the copy of it >>> I took >>> > right before the error gets thrown and it is deleted. >>> >>> Hm, yes, that is not helpful. Do you get to see more in terms of errors >>> if you do >>>make VERBOSE=1 >>> ? At the least, you would get to see which command is being executed, >>> and you >>> could do so by hand on the command line to possibly get the full >>> doxygen.log. >>> >>> >>> > I'm not sure if it makes a difference, but I'm building this on a mac >>> where I >>> > am using a terminal that is launched by the deal.II app. >>> >>> That doesn't trigger anything for me :-( >>> >>> Best >>> W. >>> >>> >>> -- >>> >>> Wolfgang Bangerth email: bang...@colostate.edu >>> www: >>> http://www.math.colostate.edu/~bangerth/ >>> >>> -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Announcing the deal.II Code Gallery
I ran "make" again and attached the outputs fm the terminal into make.log I also ran "make install" and attached the outputs from the into make_install.log It seems they are failing at different points... but I'm not sure whats going wrong.. Thanks, Mike On Monday, March 6, 2017 at 10:58:28 PM UTC-5, Wolfgang Bangerth wrote: > > On 03/06/2017 08:14 PM, Michael Harmon wrote: > > The doxygen.log file seems to get deleted... but here's the copy of it I > took > > right before the error gets thrown and it is deleted. > > Hm, yes, that is not helpful. Do you get to see more in terms of errors if > you do >make VERBOSE=1 > ? At the least, you would get to see which command is being executed, and > you > could do so by hand on the command line to possibly get the full > doxygen.log. > > > > I'm not sure if it makes a difference, but I'm building this on a mac > where I > > am using a terminal that is launched by the deal.II app. > > That doesn't trigger anything for me :-( > > Best > W. > > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. /usr/local/Cellar/cmake/3.6.0_1/bin/cmake -H/Users/Mike/Desktop/dealii-8.4.1 -B/Users/Mike/Desktop/dealii-8.4.1/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/Cellar/cmake/3.6.0_1/bin/cmake -E cmake_progress_start /Users/Mike/Desktop/dealii-8.4.1/build/CMakeFiles /Users/Mike/Desktop/dealii-8.4.1/build/CMakeFiles/progress.marks /Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/Makefile2 all /Applications/Xcode.app/Contents/Developer/usr/bin/make -f cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/build.make cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/depend cd /Users/Mike/Desktop/dealii-8.4.1/build && /usr/local/Cellar/cmake/3.6.0_1/bin/cmake -E cmake_depends "Unix Makefiles" /Users/Mike/Desktop/dealii-8.4.1 /Users/Mike/Desktop/dealii-8.4.1/cmake/scripts /Users/Mike/Desktop/dealii-8.4.1/build /Users/Mike/Desktop/dealii-8.4.1/build/cmake/scripts /Users/Mike/Desktop/dealii-8.4.1/build/cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/DependInfo.cmake --color= /Applications/Xcode.app/Contents/Developer/usr/bin/make -f cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/build.make cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/build make[2]: Nothing to be done for `cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/build'. [ 0%] Built target expand_instantiations_exe /Applications/Xcode.app/Contents/Developer/usr/bin/make -f doc/CMakeFiles/doxygen_headers.dir/build.make doc/CMakeFiles/doxygen_headers.dir/depend cd /Users/Mike/Desktop/dealii-8.4.1/build && /usr/local/Cellar/cmake/3.6.0_1/bin/cmake -E cmake_depends "Unix Makefiles" /Users/Mike/Desktop/dealii-8.4.1 /Users/Mike/Desktop/dealii-8.4.1/doc /Users/Mike/Desktop/dealii-8.4.1/build /Users/Mike/Desktop/dealii-8.4.1/build/doc /Users/Mike/Desktop/dealii-8.4.1/build/doc/CMakeFiles/doxygen_headers.dir/DependInfo.cmake --color= /Applications/Xcode.app/Contents/Developer/usr/bin/make -f doc/CMakeFiles/doxygen_headers.dir/build.make doc/CMakeFiles/doxygen_headers.dir/build make[2]: Nothing to be done for `doc/CMakeFiles/doxygen_headers.dir/build'. [ 0%] Built target doxygen_headers /Applications/Xcode.app/Contents/Developer/usr/bin/make -f doc/doxygen/code-gallery/CMakeFiles/build_code-gallery_h.dir/build.make doc/doxygen/code-gallery/CMakeFiles/build_code-gallery_h.dir/depend cd /Users/Mike/Desktop/dealii-8.4.1/build && /usr/local/Cellar/cmake/3.6.0_1/bin/cmake -E cmake_depends "Unix Makefiles" /Users/Mike/Desktop/dealii-8.4.1 /Users/Mike/Desktop/dealii-8.4.1/doc/doxygen/code-gallery /Users/Mike/Desktop/dealii-8.4.1/build /Users/Mike/Desktop/dealii-8.4.1/build/doc/doxygen/code-gallery /Users/Mike/Desktop/dealii-8.4.1/build/doc/doxygen/code-gallery/CMakeFiles/build_code-gallery_h.dir/DependInfo.cmake --color= /Applications/Xcode.app/Contents/Developer/usr/bin/make -f doc/doxygen/code-gallery/CMakeFiles/build_code-gallery_h.dir/build.make doc/doxygen/code-gallery/CMakeFiles/build_code-gallery_h.dir/build make[2]: Nothing
Re: [deal.II] Re: Announcing the deal.II Code Gallery
The doxygen.log file seems to get deleted... but here's the copy of it I took right before the error gets thrown and it is deleted. I'm not sure if it makes a difference, but I'm building this on a mac where I am using a terminal that is launched by the deal.II app. Thanks, Mike On Monday, March 6, 2017 at 6:03:47 PM UTC-5, Wolfgang Bangerth wrote: > > On 03/06/2017 03:59 PM, Michael Harmon wrote: > > down and I get the error attached as a picture... any ideas on what's > > going wrong? > > Not sure -- can you look into doxygen.log see if there are errors? Maybe > attach the whole thing? > Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. /Users/Mike/Desktop/dealii-8.4.1/source/algorithms/operator.cc:54: warning: include file operator.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH? /Users/Mike/Desktop/dealii-8.4.1/source/base/time_stepping.cc:32: warning: include file time_stepping.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH? /Users/Mike/Desktop/dealii-8.4.1/source/dofs/dof_objects.cc:69: warning: include file dof_objects.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH? /Users/Mike/Desktop/dealii-8.4.1/source/fe/fe_values.cc:1809: warning: include file fe_values.decl.1.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH? /Users/Mike/Desktop/dealii-8.4.1/source/fe/fe_values.cc:1878: warning: include file fe_values.decl.2.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH? /Users/Mike/Desktop/dealii-8.4.1/source/fe/fe_values.cc:1981: warning: include file fe_values.decl.2.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH? /Users/Mike/Desktop/dealii-8.4.1/source/grid/tria_objects.cc:467: warning: include file tria_objects.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH? /Users/Mike/Desktop/dealii-8.4.1/source/lac/trilinos_vector_base.cc:547: warning: include file trilinos_vector_base.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH? /Users/Mike/Desktop/dealii-8.4.1/source/numerics/dof_output_operator.cc:37: warning: include file dof_output_operator.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH? /Users/Mike/Desktop/dealii-8.4.1/source/numerics/fe_field_function.cc:35: warning: include file fe_field_function.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH? /Users/Mike/Desktop/dealii-8.4.1/source/opencascade/boundary_lib.cc:257: warning: include file boundary_lib.inst not found, perhaps you forgot to add its directory to INCLUDE_PATH?
[deal.II] Re: Announcing the deal.II Code Gallery
actually, i am having issues... When I build the documentation on my local machine without the code-gallery file everything works. However, with the code-gallery, it breaks <https://lh3.googleusercontent.com/-S7wEGyrweTo/WL3p2fpcAkI/B0c/e1qzh38-39UxUfqMJpbQG-M9rMuq9sVugCLcB/s1600/doxygen_error.png> down and I get the error attached as a picture... any ideas on what's going wrong? On Wednesday, March 1, 2017 at 12:34:52 AM UTC-5, Jean-Paul Pelteret wrote: > > Wolfgang's answer to Michael's question from a duplicate post: > > >> Just check out the code gallery git repository in a directory parallel to >> the >> examples/ directory and build the deal.II documentation as described in >> the >> readme. It will pick up the code gallery and create joint documentation >> for >> the tutorial and the code gallery. >> >> Best >> W. > > > On Tuesday, February 28, 2017 at 4:24:31 PM UTC+1, Michael Harmon wrote: >> >> Hi, I wanted to submit a example code to the code gallery, but was >> wondering is there a tool to see how the page will look before when all the >> doxygen comments are taken into account.. like the following: >> >> https://dealii.org/developer/doxygen/deal.II/code_gallery_cdr.html >> >> On Friday, February 12, 2016 at 2:43:10 PM UTC-5, Wolfgang Bangerth wrote: >>> >>> >>> All, >>> at the last deal.II Users and Developers Workshop last August, we had a >>> long discussion about ways how we can provide more starting points for >>> others to build their codes on. >>> >>> We came up with the "Code Gallery": A place where anyone can deposit >>> their codes built on deal.II so that others can take a look, and use it >>> as a starting point for their own work. Our goal is to provide a forum >>> that allows for the re-use of codes, and leads to more collaboration. >>> >>> Our experience with 16 years of sharing codes is that it brings people >>> together: someone who can see that a code you put online might be useful >>> to their project will likely want to collaborate with you, jointly >>> working on their project, and write papers together. In other words, >>> putting codes online doesn't just allow you to get credit for the work >>> you have done, but is also likely going to lead to contacts you might >>> otherwise never have made. >>> >>> This code gallery is now online, currently with three programs. You can >>> find it at >>>https://dealii.org/code-gallery.html >>>https://dealii.org/developer/doxygen/deal.II/CodeGallery.html >>> >>> The first of these pages also contains instructions on how anyone can >>> contribute to the code gallery. The purpose to doing so is purposefully >>> simple, and the requirements to uploading a code are minimal. *Please >>> consider making your code a component of the gallery!* >>> >>> Best >>> Wolfgang >>> >>> >>> PS: We have not gone through many versions of submission process yet. If >>> there are steps in the instructions at >>>https://dealii.org/code-gallery.html#instructions >>> that you think are unclear, let us work on them together! >>> >>> -- >>> >>> Wolfgang Bangerth email:bang...@math.tamu.edu >>> www: >>> http://www.math.tamu.edu/~bangerth/ >>> >>> -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Announcing the deal.II Code Gallery
doh. thanks! On Wednesday, March 1, 2017 at 12:34:52 AM UTC-5, Jean-Paul Pelteret wrote: > > Wolfgang's answer to Michael's question from a duplicate post: > > >> Just check out the code gallery git repository in a directory parallel to >> the >> examples/ directory and build the deal.II documentation as described in >> the >> readme. It will pick up the code gallery and create joint documentation >> for >> the tutorial and the code gallery. >> >> Best >> W. > > > On Tuesday, February 28, 2017 at 4:24:31 PM UTC+1, Michael Harmon wrote: >> >> Hi, I wanted to submit a example code to the code gallery, but was >> wondering is there a tool to see how the page will look before when all the >> doxygen comments are taken into account.. like the following: >> >> https://dealii.org/developer/doxygen/deal.II/code_gallery_cdr.html >> >> On Friday, February 12, 2016 at 2:43:10 PM UTC-5, Wolfgang Bangerth wrote: >>> >>> >>> All, >>> at the last deal.II Users and Developers Workshop last August, we had a >>> long discussion about ways how we can provide more starting points for >>> others to build their codes on. >>> >>> We came up with the "Code Gallery": A place where anyone can deposit >>> their codes built on deal.II so that others can take a look, and use it >>> as a starting point for their own work. Our goal is to provide a forum >>> that allows for the re-use of codes, and leads to more collaboration. >>> >>> Our experience with 16 years of sharing codes is that it brings people >>> together: someone who can see that a code you put online might be useful >>> to their project will likely want to collaborate with you, jointly >>> working on their project, and write papers together. In other words, >>> putting codes online doesn't just allow you to get credit for the work >>> you have done, but is also likely going to lead to contacts you might >>> otherwise never have made. >>> >>> This code gallery is now online, currently with three programs. You can >>> find it at >>>https://dealii.org/code-gallery.html >>>https://dealii.org/developer/doxygen/deal.II/CodeGallery.html >>> >>> The first of these pages also contains instructions on how anyone can >>> contribute to the code gallery. The purpose to doing so is purposefully >>> simple, and the requirements to uploading a code are minimal. *Please >>> consider making your code a component of the gallery!* >>> >>> Best >>> Wolfgang >>> >>> >>> PS: We have not gone through many versions of submission process yet. If >>> there are steps in the instructions at >>>https://dealii.org/code-gallery.html#instructions >>> that you think are unclear, let us work on them together! >>> >>> -- >>> >>> Wolfgang Bangerth email:bang...@math.tamu.edu >>> www: >>> http://www.math.tamu.edu/~bangerth/ >>> >>> -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Announcing the deal.II Code Gallery
Hi, I wanted to submit a example code to the code gallery, but was wondering is there a tool to see how the page will look before when all the doxygen comments are taken into account.. like the following: https://dealii.org/developer/doxygen/deal.II/code_gallery_cdr.html On Friday, February 12, 2016 at 2:43:10 PM UTC-5, Wolfgang Bangerth wrote: > > > All, > at the last deal.II Users and Developers Workshop last August, we had a > long discussion about ways how we can provide more starting points for > others to build their codes on. > > We came up with the "Code Gallery": A place where anyone can deposit > their codes built on deal.II so that others can take a look, and use it > as a starting point for their own work. Our goal is to provide a forum > that allows for the re-use of codes, and leads to more collaboration. > > Our experience with 16 years of sharing codes is that it brings people > together: someone who can see that a code you put online might be useful > to their project will likely want to collaborate with you, jointly > working on their project, and write papers together. In other words, > putting codes online doesn't just allow you to get credit for the work > you have done, but is also likely going to lead to contacts you might > otherwise never have made. > > This code gallery is now online, currently with three programs. You can > find it at >https://dealii.org/code-gallery.html >https://dealii.org/developer/doxygen/deal.II/CodeGallery.html > > The first of these pages also contains instructions on how anyone can > contribute to the code gallery. The purpose to doing so is purposefully > simple, and the requirements to uploading a code are minimal. *Please > consider making your code a component of the gallery!* > > Best > Wolfgang > > > PS: We have not gone through many versions of submission process yet. If > there are steps in the instructions at >https://dealii.org/code-gallery.html#instructions > that you think are unclear, let us work on them together! > > -- > > Wolfgang Bangerth email:bang...@math.tamu.edu > > www: http://www.math.tamu.edu/~bangerth/ > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: possible memory leak using TrilinosWrappers direct solver?
Is your matrix updating at every time step or just the right hand side
vector?
If its just the right hand side vector is changing, the development version
of dealii has the ability to factorize the matrix once
and then just do solve(x,b) at every time step. I'm not sure, but it Might
help.
On Monday, January 30, 2017 at 9:41:47 PM UTC-5, femFluid wrote:
>
> hi, dear all,
>
> i am using trilino's direct solver interface to solve a time-dependent
> problem. I realized that
> when the number of iterations increases, the memory usage also increases.
> This increase
> does not arise when turning the solver off, so just assembling the
> matrices.
>
> At the beginning, i used the following subroutine at every time step,
>
>{
> deallog.push("DirectKLU");
> TrilinosWrappers::SolverDirect::AdditionalData data;
> data.solver_type = "Amesos_Klu";
> SolverControl solver_control (1000, 1e-10);
> TrilinosWrappers::SolverDirect solver(solver_control, data);
> solver.solve (matrix, solution, rhs);
> thick_constraints.distribute (thick_solution);
> }
>
> then i realized that the memory might be allocated every time when
> defining TrilinosWrappers::SolverDirect solver(.), which is not
> released.
> Then I predefine the solver in a namespace, which is the used by calling
> solver.solve (matrix, solution, rhs) at each step. Still, the memory
> leakage
> occurs.
>
> I also tried to use "Amesos_Mumps", the problem still exists. I tried to
> see the documentation of Amesos, i realized that when amesos solver
> finished solving, there is a procedure 'delete solver' after. May I ask
> whether
> such a member function exists in dealII wrappers? Thanks in advance,
>
> best,
> lailai
>
--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
https://groups.google.com/d/forum/dealii?hl=en
---
You received this message because you are subscribed to the Google Groups
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: question on doxygen
Just on my own program. On Wednesday, November 16, 2016 at 9:44:59 AM UTC-5, Wolfgang Bangerth wrote: > > On 11/16/2016 07:41 AM, Michael Harmon wrote: > > > > I had to change the http from: > > > > MATHJAX_REPATH = http://cdn.mathjax.org/mathjax/latest/ > > > > to https: > > > > MATHJAX_REPATH = http*s*://cdn.mathjax.org/mathjax/latest/ > > > > Michael, > where did you need to change this? In deal.II somewhere? Or just in your > own > program? > > Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: question on doxygen
Thanks Timo! I had to change the http from: MATHJAX_REPATH = http://cdn.mathjax.org/mathjax/latest/ to https: MATHJAX_REPATH = http*s*://cdn.mathjax.org/mathjax/latest/ On Tuesday, November 15, 2016 at 12:03:55 PM UTC-5, Michael Harmon wrote: > > Hi, > > I used deal for my phd work, loved using it and wanted to put my code up > on github. I spent a lot of time documenting it with doxygen, but latex > equations only work on my local machine and not on github: > > https://mdh266.github.io/PECS/index.html > > Anyone else have this issue? > > Thanks! > > Mike > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: Publications based on deal.II
Thank you! -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Publications based on deal.II
Not sure if its too late for this, but here are some publications thanks to
deal.ii!
@Article{HaGaRe-JCP2016,
Title= Numerical algorithms based on Galerkin methods
for the modeling of reactive interfaces in photoelectrochemical (PEC) solar
cells},
Author = {M. Harmon and I. M. Gamba and K. Ren.},
Journal = {Journal of Computational Physics},
Year = {2016}
}
@phdthesis{Harmon2016,
Title= Numerical algorithms based on Galerkin methods
for the modeling of reactive interfaces in photoelectrochemical (PEC) solar
cells},
Author = {Michael Harmon},
School = {University of Texas at Austin},
Year = {2016}
}
On Sunday, January 17, 2016 at 6:09:44 PM UTC-5, Wolfgang Bangerth wrote:
>
>
> All,
>
> as you may know, we try to list all publications based on deal.II at
> http://dealii.org/publications.html
> <http://www.google.com/url?q=http%3A%2F%2Fdealii.org%2Fpublications.html&sa=D&sntz=1&usg=AFQjCNFCMbrX9XZ7uWlZ4QbchtIN51_2KA>
>
> We use this list to justify the effort we spend on writing this software,
> both
> to our universities as well as the funding agencies that support its
> development.
>
> In anticipation of the next release, we would like to update this page. If
> you
> have (or know of) a publication that uses deal.II for numerical results
> and
> that isn't already listed, please let us know so we can put it on there.
> For
> this purpose, publications also include MSc, Diploma or PhD theses, or
> anything else that may seem appropriate.
>
> Thanks!
>Wolfgang
>
> --
>
> Wolfgang Bangerth email:bang...@math.tamu.edu
>
> www: http://www.math.tamu.edu/~bangerth/
>
>
--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
https://groups.google.com/d/forum/dealii?hl=en
---
You received this message because you are subscribed to the Google Groups
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
[deal.II] question on doxygen
Hi, I used deal for my phd work, loved using it and wanted to put my code up on github. I spent a lot of time documenting it with doxygen, but latex equations only work on my local machine and not on github: https://mdh266.github.io/PECS/index.html Anyone else have this issue? Thanks! Mike -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Using the solution from one problem as a boundary condition in another problem with matching mesh on the boundary
Nice! Good luck with Gmsh! On Tuesday, August 23, 2016 at 11:10:46 AM UTC-4, krei wrote: > > Thanks for the response. I have a more-or-less working version where the > whole thing is solved together by Newton's method, but I bet solving > electric field separately gives a good performance boost. I will try to > fiddle with it, however, generating multiple meshes with matching boundary > for testing is not very trivial (GMSH doesn't let you do this, as far as I > know), I have to investigate if I can mark the elements in gmsh and then > separate the meshes in deal ii. > > On Tuesday, August 23, 2016 at 5:55:32 PM UTC+3, Michael Harmon wrote: >> >> Hey, >> >> I had a similar problem: PDES in separate domains that are coupled >> through an interface as a boundary condition. You can go about it using >> one triangulation; I attempted to do this at first, but ended up using >> multiple meshes. The fact you have matching meshes on the boundary is good. >> What you want to do is create two meshes and two dof handlers. Initially >> you need to create a std::map to create a bijection between the faces on >> the different meshes that are on the interface/ connecting boundary. When >> you are assembling the coupling terms on the boundary condition you can get >> the corresponding face in the other mesh and initialize the fe_values on >> that face and get its values on the face to assemble the boundary >> conditions. >> >> Check out: >> >> https://groups.google.com/forum/#!searchin/dealii/multiple$20triangulations%7Csort:relevance/dealii/R64BUBhyFf0/LbbxH9v8GgAJ >> >> If it helps I can also send you my code to see how to do this using >> deal.ii >> >> Best, >> >> Mike >> >> On Thursday, July 28, 2016 at 2:17:12 PM UTC-4, krei wrote: >>> >>> >>> The problem I am currently having is directly related to my previous >>> post [here]( >>> https://groups.google.com/forum/#!searchin/dealii/krei/dealii/eq_zP0jrSJU/SyQXA7A-DAAJ >>> ). >>> >>> The physics are exactly the same as described in that thread: I have a >>> two domain system: vacuum and metal, both domains have their own meshes. >>> [Here is a picture](http://i.imgur.com/CejXi1y.png). The meshes are >>> exactly matching on the boundary. I want to solve the Laplace equation for >>> electric fields in the vacuum part (does not depend on anything in the >>> metal part) and then use the electric field as a boundary condition to the >>> metal part. >>> >>> I am currently using VectorTools::point_gradient to evaluate the >>> electric field from the Laplace problem in the quadrature points of the >>> boundary cell faces of the metal mesh. As a result, it takes over an hour >>> to assemble the system (solving takes less than a second). >>> >>> Now, considering that the mesh is exactly matching at the boundary (all >>> the quadrature points etc), how could I efficiently evaluate the electric >>> field at the boundary? >>> >>> And I apologize if I'm mistaken, but there doesn't seem to be any >>> tutorials on these kinds of problems where you have multiple domains with >>> multiple meshes. Or is it usually done by using a single mesh and somehow >>> defining different domains in that mesh? (haven't delved deeply into >>> Step-46, but there they do something like this, right?) >>> >> -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Using the solution from one problem as a boundary condition in another problem with matching mesh on the boundary
Hey, I had a similar problem: PDES in separate domains that are coupled through an interface as a boundary condition. You can go about it using one triangulation; I attempted to do this at first, but ended up using multiple meshes. The fact you have matching meshes on the boundary is good. What you want to do is create two meshes and two dof handlers. Initially you need to create a std::map to create a bijection between the faces on the different meshes that are on the interface/ connecting boundary. When you are assembling the coupling terms on the boundary condition you can get the corresponding face in the other mesh and initialize the fe_values on that face and get its values on the face to assemble the boundary conditions. Check out: https://groups.google.com/forum/#!searchin/dealii/multiple$20triangulations%7Csort:relevance/dealii/R64BUBhyFf0/LbbxH9v8GgAJ If it helps I can also send you my code to see how to do this using deal.ii Best, Mike On Thursday, July 28, 2016 at 2:17:12 PM UTC-4, krei wrote: > > > The problem I am currently having is directly related to my previous post > [here]( > https://groups.google.com/forum/#!searchin/dealii/krei/dealii/eq_zP0jrSJU/SyQXA7A-DAAJ > ). > > The physics are exactly the same as described in that thread: I have a two > domain system: vacuum and metal, both domains have their own meshes. [Here > is a picture](http://i.imgur.com/CejXi1y.png). The meshes are exactly > matching on the boundary. I want to solve the Laplace equation for electric > fields in the vacuum part (does not depend on anything in the metal part) > and then use the electric field as a boundary condition to the metal part. > > I am currently using VectorTools::point_gradient to evaluate the electric > field from the Laplace problem in the quadrature points of the boundary > cell faces of the metal mesh. As a result, it takes over an hour to > assemble the system (solving takes less than a second). > > Now, considering that the mesh is exactly matching at the boundary (all > the quadrature points etc), how could I efficiently evaluate the electric > field at the boundary? > > And I apologize if I'm mistaken, but there doesn't seem to be any > tutorials on these kinds of problems where you have multiple domains with > multiple meshes. Or is it usually done by using a single mesh and somehow > defining different domains in that mesh? (haven't delved deeply into > Step-46, but there they do something like this, right?) > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
